def test_cosym(dials_data, run_in_tmpdir, space_group, engine):
mcp = dials_data("multi_crystal_proteinase_k")
args = ["space_group=" + str(space_group), "seed=0", f"engine={engine}"]
for i in [1, 2, 3, 4, 5, 7, 8, 10]:
args.append(mcp.join("experiments_%d.json" % i).strpath)
args.append(mcp.join("reflections_%d.pickle" % i).strpath)
dials_cosym.run(args=args)
assert os.path.isfile("symmetrized.refl")
assert os.path.isfile("symmetrized.expt")
experiments = load.experiment_list("symmetrized.expt", check_format=False)
if space_group is None:
assert (
experiments[0].crystal.get_space_group().type().lookup_symbol() == "P 4 2 2"
)
else:
assert (
experiments[0].crystal.get_space_group().type().lookup_symbol()
== space_group
)
joint_reflections = flex.reflection_table.from_file("symmetrized.refl")
# check that there are 8 unique id and imageset_ids, and that these
# correctly correspond to each experiment
assert len(set(joint_reflections["id"])) == 8
assert len(set(joint_reflections["imageset_id"])) == 8
for id_ in range(8):
sel = joint_reflections["id"] == id_
assert set(joint_reflections["imageset_id"].select(sel)) == {id_}
def test_cosym_partial_dataset_raises_sorry(dials_data, run_in_tmpdir, capsys):
"""Test how cosym handles partial/bad datasets."""
mcp = dials_data("multi_crystal_proteinase_k")
args = ["renamed.refl", mcp.join("experiments_8.json").strpath]
r2 = flex.reflection_table.from_file(mcp.join("reflections_10.pickle").strpath)
r2["partiality"] = flex.double(r2.size(), 0.1)
r2.as_file("renamed2.refl")
args.append("renamed2.refl")
args.append(mcp.join("experiments_10.json").strpath)
with pytest.raises(Sorry):
dials_cosym.run(args=args)
def test_cosym(dials_data, run_in_tmpdir, space_group):
mcp = dials_data("multi_crystal_proteinase_k")
args = ["space_group=" + str(space_group)]
for i in [1, 2, 3, 4, 5, 7, 8, 10]:
args.append(mcp.join("experiments_%d.json" % i).strpath)
args.append(mcp.join("reflections_%d.pickle" % i).strpath)
dials_cosym.run(args=args)
assert os.path.isfile("symmetrized.refl")
assert os.path.isfile("symmetrized.expt")
experiments = load.experiment_list("symmetrized.expt", check_format=False)
if space_group is None:
assert (experiments[0].crystal.get_space_group().type().lookup_symbol(
) == "P 4 2 2")
else:
assert (experiments[0].crystal.get_space_group().type().lookup_symbol(
) == space_group)
def test_cosym_resolution_filter_excluding_datasets(dials_data, run_in_tmpdir):
mcp = dials_data("multi_crystal_proteinase_k", pathlib=True)
args = ["space_group=P4", "seed=0", "d_min=20.0"]
for i in [1, 2, 3, 4, 5, 7, 8, 10]:
args.append(os.fspath(mcp / f"experiments_{i}.json"))
args.append(os.fspath(mcp / f"reflections_{i}.pickle"))
dials_cosym.run(args=args)
assert pathlib.Path("symmetrized.refl").is_file()
assert pathlib.Path("symmetrized.expt").is_file()
joint_reflections = flex.reflection_table.from_file("symmetrized.refl")
# check that there are 8 unique id and imageset_ids, and that these
# correctly correspond to each experiment
assert set(joint_reflections["id"]) == {0, 1, 2, 3, 4, 5, 6}
assert len(set(joint_reflections["imageset_id"])) == 7
for id_ in range(7):
sel = joint_reflections["id"] == id_
assert set(joint_reflections["imageset_id"].select(sel)) == {id_}
def test_cosym_partial_dataset(dials_data, run_in_tmpdir):
"""Test how cosym handles partial/bad datasets."""
mcp = dials_data("multi_crystal_proteinase_k")
args = []
for i in [1, 2]:
args.append(mcp.join("experiments_%d.json" % i).strpath)
args.append(mcp.join("reflections_%d.pickle" % i).strpath)
# Make one dataset that will be removed in prefiltering
r = flex.reflection_table.from_file(mcp.join("reflections_8.pickle").strpath)
r["partiality"] = flex.double(r.size(), 0.1)
r.as_file("renamed.refl")
args.append("renamed.refl")
args.append(mcp.join("experiments_8.json").strpath)
# Add another good dataset at the end of the input list
args.append(mcp.join("experiments_10.json").strpath)
args.append(mcp.join("reflections_10.pickle").strpath)
dials_cosym.run(args=args)
assert os.path.exists("symmetrized.refl")
assert os.path.exists("symmetrized.expt")
experiments = load.experiment_list("symmetrized.expt", check_format=False)
assert len(experiments) == 3
def _run(self):
try:
run(self.cmd)
except Exception as e:
self.logger.error('Dials cosym execution found an exception: {}'.format(e))
def test_synthetic(
space_group,
unit_cell,
dimensions,
sample_size,
use_known_space_group,
use_known_lattice_group,
run_in_tmpdir,
):
space_group = sgtbx.space_group_info(space_group).group()
if unit_cell is not None:
unit_cell = uctbx.unit_cell(unit_cell)
experiments, reflections, _ = generate_experiments_reflections(
space_group=space_group,
unit_cell=unit_cell,
unit_cell_volume=10000,
sample_size=sample_size,
map_to_p1=True,
d_min=1.5,
)
experiments.as_json("tmp.expt")
expt_file = "tmp.expt"
joint_table = flex.reflection_table()
for r in reflections:
joint_table.extend(r)
joint_table.as_file("tmp.refl")
refl_file = "tmp.refl"
args = [
expt_file,
refl_file,
"output.experiments=symmetrized.expt",
"output.reflections=symmetrized.refl",
"output.html=cosym.html",
"output.json=cosym.json",
]
if use_known_space_group:
args.append(f"space_group={space_group.info()}")
if use_known_lattice_group:
args.append(f"lattice_group={space_group.info()}")
if dimensions is not None:
args.append(f"dimensions={dimensions}")
dials_cosym.run(args=args)
assert os.path.isfile("symmetrized.refl")
assert os.path.isfile("symmetrized.expt")
assert os.path.isfile("cosym.html")
assert os.path.isfile("cosym.json")
cosym_expts = load.experiment_list("symmetrized.expt", check_format=False)
assert len(cosym_expts) == len(experiments)
for expt in cosym_expts:
if unit_cell is not None:
assert expt.crystal.get_unit_cell().parameters() == pytest.approx(
unit_cell.parameters()
)
if (
str(expt.crystal.get_space_group().info()) == "P 6 2 2"
and str(space_group.info()) == "P 3 2 1"
):
# This is fine
continue
assert str(expt.crystal.get_space_group().info()) == str(space_group.info())
assert expt.crystal.get_space_group() == space_group